positional arguments:¶

cwl_document

path or URL to a CWL Workflow, CommandLineTool, or ExpressionTool. If the `inputs_object` has a `cwl:tool` field indicating the path or URL to the cwl_document, then the `workflow` argument is optional.

inputs_object

path or URL to a YAML or JSON formatted description of the required input values for the given `cwl_document`.

optional arguments:¶

-h, --help

show this help message and exit

--basedir BASEDIR

--outdir OUTDIR

Output directory, default current directory

--parallel

[experimental] Run jobs in parallel.

--preserve-environment ENVVAR

Preserve specific environment variable when running CommandLineTools. May be provided multiple times.

--preserve-entire-environment

Preserve all environment variable when running CommandLineTools.

--rm-container

Delete Docker container used by jobs after they exit (default)

--leave-container

Do not delete Docker container used by jobs after they exit

--tmpdir-prefix TMPDIR_PREFIX

Path prefix for temporary directories

--tmp-outdir-prefix TMP_OUTDIR_PREFIX

Path prefix for intermediate output directories

--cachedir CACHEDIR

Directory to cache intermediate workflow outputs to avoid recomputing steps.

--rm-tmpdir

Delete intermediate temporary directories (default)

--leave-tmpdir

Do not delete intermediate temporary directories

--move-outputs

Move output files to the workflow output directory and delete intermediate output directories (default).

--leave-outputs

Leave output files in intermediate output directories.

--copy-outputs

Copy output files to the workflow output directory, don't delete intermediate output directories.

--enable-pull

Try to pull Docker images

--disable-pull

Do not try to pull Docker images

--rdf-serializer RDF_SERIALIZER

Output RDF serialization format used by --print-rdf (one of turtle (default), n3, nt, xml)

--eval-timeout EVAL_TIMEOUT

Time to wait for a Javascript expression to evaluate before giving an error, default 20s.

--print-rdf

Print corresponding RDF graph for workflow and exit

--print-dot

Print workflow visualization in graphviz format and exit

--print-pre

Print CWL document after preprocessing.

--print-deps

Print CWL document dependencies.

--print-input-deps

Print input object document dependencies.

--pack

Combine components into single document and print.

--version

Print version and exit

--validate

Validate CWL document only.

--print-supported-versions

Print supported CWL specs.

--print-subgraph

Print workflow subgraph that will execute (can combine with --target)

--print-targets

Print targets (output parameters)

--strict

Strict validation (unrecognized or out of place fields are error)

--non-strict

Lenient validation (ignore unrecognized fields)

--skip-schemas

Skip loading of schemas

--verbose

Default logging

--quiet

Only print warnings and errors.

--debug

Print even more logging

--strict-memory-limit

When running with software containers and the Docker engine, pass either the calculated memory allocation from ResourceRequirements or the default of 1 gigabyte to Docker's --memory option.

--timestamps

Add timestamps to the errors, warnings, and notifications.

--js-console

Enable javascript console output

--user-space-docker-cmd CMD

(Linux/OS X only) Specify a user space docker command (like udocker or dx-docker) that will be used to call 'pull' and 'run'

--singularity

[experimental] Use Singularity runtime for running containers. Requires Singularity v2.3.2+ and Linux with kernel version v3.18+ or with overlayfs support backported.

--no-container

Do not execute jobs in a Docker container, even when `DockerRequirement` is specified under `hints`.

--tool-help

Print command line help for tool

--relative-deps {primary,cwd}

When using --print-deps, print paths relative to primary file or current working directory.

--enable-dev

Enable loading and running development versions of CWL spec.

--enable-ext

Enable loading and running cwltool extensions to CWL spec.

--default-container DEFAULT_CONTAINER

Specify a default docker container that will be used if the workflow fails to specify one.

--no-match-user

Disable passing the current uid to `docker run --user`

--custom-net CUSTOM_NET

Passed to `docker run` as the '--net' parameter when NetworkAccess is true.

--enable-ga4gh-tool-registry

Enable resolution using GA4GH tool registry API

--disable-ga4gh-tool-registry

Disable resolution using GA4GH tool registry API

--add-ga4gh-tool-registry GA4GH_TOOL_REGISTRIES

Add a GA4GH tool registry endpoint to use for resolution, default ['https://dockstore.org/api']

--on-error {stop,continue}

Desired workflow behavior when a step fails. One of 'stop' (do not submit any more steps) or 'continue' (may submit other steps that are not downstream from the error). Default is 'stop'.

--compute-checksum

Compute checksum of contents while collecting outputs

--no-compute-checksum

Do not compute checksum of contents while collecting outputs

--relax-path-checks

Relax requirements on path names to permit spaces and hash characters.

--make-template

Generate a template input object

--force-docker-pull

Pull latest docker image even if it is locally present

--no-read-only

Do not set root directory in the container as readonly

--overrides OVERRIDES

Read process requirement overrides from file.

--target TARGET, -t TARGET

Only execute steps that contribute to listed targets (can provide more than once).

Options for recording the Docker container identifier into a file.:¶

--cidfile-dir CIDFILE_DIR

Store the Docker container ID into a file in the specified directory.

--cidfile-prefix CIDFILE_PREFIX

Specify a prefix to the container ID filename. Final file name will be followed by a timestamp. The default is no prefix.